When Maj. Leonard's team vanishes during an off-world exploration, Sheppard's team is hot on their trail, bringing along Dr. Beckett and three Marines for backup. On the forested planet, they're greeted by the grisly sight of several Genii soldiers, long dead, who killed each other. Deeper into the forest, they find a cavelike bunker containing a mysterious Wraith electromagnetic generator that is emitting a modulated ultra-low-frequency pulse.
Leonard's men lie dead nearby. The video footage they shot reveals that they believed they were under alien attack - but they were actually killed by their commander, Leonard. Unnerved, Sheppard orders his team to bear the bodies back to Atlantis and return with reinforcements, but Leonard has sabotaged the stargate's DHD. When the team tries to dial home, the device blows up, killing one of the Marines and injuring the other two, Kagan and Barroso.
Now trapped on the planet with their berserk former comrade, Sheppard's team retreats to the bunker, where McKay guesses that the Wraith EM device provokes dangerous delusional behavior in humans. Suddenly, Ronon spots two Wraith in the woods nearby and gives chase. Sheppard and Teyla follow, only to discover that Ronon is actually pursuing Leonard, who is still irrationally bent on killing them all. Leonard shoots Teyla in the leg before escaping with the delusional Ronon on his heels. And as Sheppard binds Teyla's serious injury, he briefly hallucinates that she's an old Air Force comrade, Capt. Lyle Holland. The Wraith device is affecting him, too. Moments later, Leonard - convinced that he's hopelessly surrounded by enemies - kills himself.
At the Wraith bunker, Beckett watches in agony as Kagan dies, only to be stunned when Kagan returns to life and Barroso turns out to be dead instead. Wracked with delusions, the doctor can't tell which patient actually needs his care. McKay, meanwhile, struggles to shut down the generator, but it seems to defeat him at every turn.
In the forest, Teyla watches in pain and concern as Sheppard succumbs to his vision of the past. He believes that he's trapped with Capt. Holland in the Afghan desert, surrounded by Taliban fighters. Nearby, Ronon stalks closer, convinced that he's hunting Wraith enemies. When the two finally spot each other, Sheppard sees a Taliban soldier and Ronon sees a Wraith. They start shooting, and neither man's going to quit until his enemy is dead.